{"id":"https://openalex.org/W2410978489","doi":"https://doi.org/10.1186/s12859-016-1040-7","title":"Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis","display_name":"Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis","publication_year":2016,"publication_date":"2016-06-01","ids":{"openalex":"https://openalex.org/W2410978489","doi":"https://doi.org/10.1186/s12859-016-1040-7","mag":"2410978489","pmid":"https://pubmed.ncbi.nlm.nih.gov/27295045"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-016-1040-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1040-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1040-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1040-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023050756","display_name":"Panagiotis Chouvardas","orcid":"https://orcid.org/0000-0003-1527-3151"},"institutions":[{"id":"https://openalex.org/I6820528","display_name":"Alexander Fleming Biomedical Sciences Research Center","ror":"https://ror.org/013x0ky90","country_code":"GR","type":"facility","lineage":["https://openalex.org/I6820528"]},{"id":"https://openalex.org/I72702400","display_name":"Athens State University","ror":"https://ror.org/01zx16v02","country_code":"US","type":"education","lineage":["https://openalex.org/I72702400"]},{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]}],"countries":["GR","US"],"is_corresponding":false,"raw_author_name":"Panagiotis Chouvardas","raw_affiliation_strings":["Biomedical Sciences Research Center \"Alexander Fleming\", Vari, 16672, Greece","Department of Physiology, Medical School, University of Athens, Athens, 11527, Greece","Biomedical Sciences Research Center \u201cAlexander Fleming\u201d, Vari, Greece","Department of Physiology, Medical School, University of Athens, Athens, Greece"],"affiliations":[{"raw_affiliation_string":"Biomedical Sciences Research Center \"Alexander Fleming\", Vari, 16672, Greece","institution_ids":["https://openalex.org/I6820528"]},{"raw_affiliation_string":"Department of Physiology, Medical School, University of Athens, Athens, 11527, Greece","institution_ids":["https://openalex.org/I72702400"]},{"raw_affiliation_string":"Biomedical Sciences Research Center \u201cAlexander Fleming\u201d, Vari, Greece","institution_ids":["https://openalex.org/I6820528"]},{"raw_affiliation_string":"Department of Physiology, Medical School, University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062268324","display_name":"George Kollias","orcid":"https://orcid.org/0000-0003-1867-3150"},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]},{"id":"https://openalex.org/I6820528","display_name":"Alexander Fleming Biomedical Sciences Research Center","ror":"https://ror.org/013x0ky90","country_code":"GR","type":"facility","lineage":["https://openalex.org/I6820528"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"George Kollias","raw_affiliation_strings":["Department of Physiology, School of Medicine, National and Kapodistrian University of Athens, Athens, 11527, Greece","Division of Immunology, Biomedical Sciences Research Center \"Alexander Fleming\", Vari, 16672, Greece","Division of Immunology, Biomedical Sciences Research Center \u201cAlexander Fleming\u201d, Vari, Greece","Department of Physiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece"],"affiliations":[{"raw_affiliation_string":"Department of Physiology, School of Medicine, National and Kapodistrian University of Athens, Athens, 11527, Greece","institution_ids":["https://openalex.org/I200777214"]},{"raw_affiliation_string":"Division of Immunology, Biomedical Sciences Research Center \"Alexander Fleming\", Vari, 16672, Greece","institution_ids":["https://openalex.org/I6820528"]},{"raw_affiliation_string":"Division of Immunology, Biomedical Sciences Research Center \u201cAlexander Fleming\u201d, Vari, Greece","institution_ids":["https://openalex.org/I6820528"]},{"raw_affiliation_string":"Department of Physiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024197769","display_name":"Christoforos Nikolaou","orcid":"https://orcid.org/0000-0003-3001-6786"},"institutions":[{"id":"https://openalex.org/I6820528","display_name":"Alexander Fleming Biomedical Sciences Research Center","ror":"https://ror.org/013x0ky90","country_code":"GR","type":"facility","lineage":["https://openalex.org/I6820528"]},{"id":"https://openalex.org/I142617266","display_name":"University of Crete","ror":"https://ror.org/00dr28g20","country_code":"GR","type":"education","lineage":["https://openalex.org/I142617266"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Christoforos Nikolaou","raw_affiliation_strings":["Biomedical Sciences Research Center \"Alexander Fleming\", Vari, 16672, Greece. cnikolaou@biology.uoc.gr","Computational Genomics Group, Department of Biology, University of Crete, Voutes Campus, Heraklion, 70013, Greece. cnikolaou@biology.uoc.gr","Computational Genomics Group, Department of Biology, University of Crete, Voutes Campus, Heraklion, Greece","Biomedical Sciences Research Center \u201cAlexander Fleming\u201d, Vari, Greece"],"affiliations":[{"raw_affiliation_string":"Biomedical Sciences Research Center \"Alexander Fleming\", Vari, 16672, Greece. cnikolaou@biology.uoc.gr","institution_ids":[]},{"raw_affiliation_string":"Computational Genomics Group, Department of Biology, University of Crete, Voutes Campus, Heraklion, 70013, Greece. cnikolaou@biology.uoc.gr","institution_ids":[]},{"raw_affiliation_string":"Computational Genomics Group, Department of Biology, University of Crete, Voutes Campus, Heraklion, Greece","institution_ids":["https://openalex.org/I142617266"]},{"raw_affiliation_string":"Biomedical Sciences Research Center \u201cAlexander Fleming\u201d, Vari, Greece","institution_ids":["https://openalex.org/I6820528"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5024197769"],"corresponding_institution_ids":["https://openalex.org/I142617266","https://openalex.org/I6820528"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.3119,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.9226599,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"17","issue":"S5","first_page":"181","last_page":"181"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/subnetwork","display_name":"Subnetwork","score":0.8963301181793213},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.693625807762146},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6398786902427673},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5956627726554871},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5532153844833374},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5186178088188171},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.4600543677806854},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.453269898891449},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.43299925327301025},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.41660308837890625},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.41303178668022156},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4123304784297943},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3796936869621277},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33194994926452637},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3238708972930908},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25195619463920593},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22559401392936707}],"concepts":[{"id":"https://openalex.org/C2780186347","wikidata":"https://www.wikidata.org/wiki/Q11414","display_name":"Subnetwork","level":2,"score":0.8963301181793213},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.693625807762146},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6398786902427673},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5956627726554871},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5532153844833374},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5186178088188171},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.4600543677806854},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.453269898891449},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.43299925327301025},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.41660308837890625},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41303178668022156},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4123304784297943},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3796936869621277},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33194994926452637},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3238708972930908},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25195619463920593},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22559401392936707},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-016-1040-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1040-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1040-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27295045","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27295045","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3872230","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4905609","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:zenodo.org:55265","is_oa":true,"landing_page_url":"https://zenodo.org/record/55265","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-016-1040-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1040-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1040-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5168646090","display_name":null,"funder_award_id":"ERC06","funder_id":"https://openalex.org/F4320321917","funder_display_name":"General Secretariat for Research and Technology"},{"id":"https://openalex.org/G6116908885","display_name":null,"funder_award_id":"2007-2013","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"},{"id":"https://openalex.org/G7168330642","display_name":null,"funder_award_id":"NSRF 2007-2013","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"},{"id":"https://openalex.org/G8557630580","display_name":null,"funder_award_id":"co-financed","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"}],"funders":[{"id":"https://openalex.org/F4320321917","display_name":"General Secretariat for Research and Technology","ror":"https://ror.org/04yeh8h63"},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2410978489.pdf","grobid_xml":"https://content.openalex.org/works/W2410978489.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W137498602","https://openalex.org/W1533049846","https://openalex.org/W1533691218","https://openalex.org/W1549935590","https://openalex.org/W1965510471","https://openalex.org/W1987909353","https://openalex.org/W2000859725","https://openalex.org/W2008620264","https://openalex.org/W2020932061","https://openalex.org/W2022554606","https://openalex.org/W2030371558","https://openalex.org/W2030903733","https://openalex.org/W2052918843","https://openalex.org/W2070050178","https://openalex.org/W2070494252","https://openalex.org/W2073253686","https://openalex.org/W2088010622","https://openalex.org/W2098264959","https://openalex.org/W2100714130","https://openalex.org/W2100859976","https://openalex.org/W2103017472","https://openalex.org/W2103796092","https://openalex.org/W2110687686","https://openalex.org/W2111164126","https://openalex.org/W2114104545","https://openalex.org/W2120568877","https://openalex.org/W2124954099","https://openalex.org/W2125523949","https://openalex.org/W2126606094","https://openalex.org/W2128219894","https://openalex.org/W2130410032","https://openalex.org/W2133465414","https://openalex.org/W2133658633","https://openalex.org/W2141458291","https://openalex.org/W2141781797","https://openalex.org/W2146412506","https://openalex.org/W2152239989","https://openalex.org/W2153624566","https://openalex.org/W2158217645","https://openalex.org/W2159482845","https://openalex.org/W2159675211","https://openalex.org/W2163480486","https://openalex.org/W2171149788","https://openalex.org/W2171322586","https://openalex.org/W2403934794","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W15348386","https://openalex.org/W2099991711","https://openalex.org/W2478888221","https://openalex.org/W2032799661","https://openalex.org/W2095452756","https://openalex.org/W2096259797","https://openalex.org/W2069695727","https://openalex.org/W2521885831","https://openalex.org/W2788913047","https://openalex.org/W1996185163"],"abstract_inverted_index":{"RNEA":[0,66],"constitutes":[1],"a":[2,12,32,59,67,72],"novel":[3,56],"computational":[4],"approach":[5],"to":[6,40],"obtain":[7],"regulatory":[8,48,63],"interactions":[9,64],"directly":[10],"from":[11,22],"genome-wide":[13],"expression":[14,77],"profile.":[15],"Its":[16],"simple":[17],"implementation,":[18],"with":[19,27],"minimal":[20],"requirements":[21],"the":[23,42,47],"user":[24],"is":[25],"coupled":[26],"easy-to-parse":[28],"enrichment":[29],"lists":[30],"and":[31,55],"subnetwork":[33],"file":[34],"that":[35],"may":[36],"be":[37],"readily":[38],"visualized":[39],"reveal":[41],"most":[43],"important":[44],"components":[45],"of":[46,52,58,62,75],"hierarchy.":[49],"The":[50],"combination":[51],"prior":[53],"information":[54],"concept":[57],"hierarchical":[60],"reconstruction":[61],"makes":[65],"very":[68],"useful":[69],"tool":[70],"for":[71],"first-level":[73],"interpretation":[74],"gene":[76],"profiles.":[78]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
